Characterizing Tumor Heterogeneity

Comprehending the sheer complexity of the molecular mechanisms underlying cancer has challenged researchers for years. The advent of molecular genetics has radically changed our understanding of cancer. We now know that cancer is a disease of the genome and we are starting to understand the molecular mechanisms that drive the transformation of a normal cell into a malignant cell. Recent technological advances, such as the possibility to analyze the genome of single cells within a tumor, is allowing us to dive even deeper into the nature of cancer, revealing a startling degree of complexity.

Until recently, it was thought that after accumulating a certain number of driver-mutations, a cell would go through a phase of clonal expansion, leading to a fairly homogeneous population of cancer cells. However, recent studies on biopsies taken from different portions of the primary tumor, as well as from metastasis, have revealed a high degree of genetic heterogeneity. Each tumor is a complex environment where different cell populations coexist. Each of these populations has its own genetic fingerprint, which leads to different phenotypes. This diversity may explain why cancer is so resistant to therapy, including more targeted therapeutic approaches. It may also explain why when patients relapse, the therapy that was successful in the first instance often becomes ineffective. In this case, the therapeutic agent puts a selective pressure on the evolution of the tumor, killing clones that carry a particular mutation but not others, allowing them to proliferate.

In this article, we explore the challenges associated with tumor heterogeneity and examine solutions that accelerate the analysis of tumors.

Back to topHow to characterize heterogeneity
To study the heterogeneous nature of tumors, several solutions are available, depending on the research objective. If the goal is to characterize the different populations present in a given sample, whole genome amplification (WGA) can be performed from single cells using the REPLI-g Single Cell Kit. This enables genetic profiling and analysis of gene expression signatures of individual cell populations.

Back to topHow to minimize the effects of heterogeneity
In some cases, for instance when analyzing both DNA and RNA from the same sample, the challenge is to limit the effect of tumor heterogeneity. To avoid analyzing DNA that originates from one population and RNA from another, it is recommended to perform the analysis from the same starting material. Solutions such as the AllPrep DNA/RNA Kit allow simultaneous isolation of DNA and RNA from a single specimen, minimizing biases introduced by the heterogeneous nature of the sample. Similarly, when dealing with very limited amounts of cells, solutions such as the new REPLI-g Cell WGA & WTA Kit provide simultaneous amplification of DNA and RNA from just 25–1000 cells.

Back to topHow to integrate data
To obtain a holistic view of mutations, copy number alterations, changes in gene expression, and the pathways affected by these events, bioinformatics tools such as Ingenuity Pathway Analysis (IPA) are employed. Combining data from genetic and gene expression profiling, Ingenuity Pathway Analysis provides a deeper insight into such data, facilitating accurate interpretation.

Back to topHow to monitor tumor evolution in real time
It can be useful to monitor the clonal composition of the tumor, especially during treatment. Traditionally, monitoring the progress and evolution of the malignancy required obtaining a biopsy sample from the patient. In addition to being a highly invasive procedure, storage and transport of biopsy samples is also not convenient. Thanks to recent advances in purification of circulating nucleic acids, it’s now possible to detect tumor-specific DNA fragments and mRNAs directly in the blood. These circulating nucleic acids are present in serum or plasma usually as short fragments, <1000 bp (DNA) or <1000 nt (RNA), and can be investigated with assays targeting specific mutations previously identified in the tumor, offering a way to monitor the relative proportion of different clones over time. The QIAamp Circulating Nucleic Acid Kit allows efficient purification of these circulating nucleic acids from human plasma or serum and other cell-free body fluids. Delivering reproducible yields, the kit provides a reliable indication of the representative population of these circulating nucleic acids in blood.